Yes on the middle shuttlecraft. I just put it there to illustrate that it is wide enough for three shuttles.
I rendered two comparison shots. One from the scene in "Journey to Babel" at the door looking into the hangar and one from the often used one for the flight deck.
In the hangar deck shot, I removed the middle shuttle and left the two (one on each side of the door) and rendered away. Neither of the two parked shuttles were visible from that vantage point so it is possible that from all the scenes we've seen in TOS that you can have two parked shuttles in the hangar deck and not be able to see them
On the flight deck, there could be room to park three more up there as well. Since the ships were suppose to have a four shuttle complement, it could work that three were in the hangar deck (2 parked by near wall, 1 on the elevator pad ready to go) and 1 stored on the flight deck near the forward wall. There would still be room for two, maybe three more shuttles without stopping up shuttle operations.
You can see my work in progress here:
Also, just for grins, I replaced the shuttles with the larger Galileo 5 from ST:V and everything still fits!
There were some compromises I did make to get everything to fit though. The flight deck is much longer than what has been drawn in any blueprint I've ever seen. Also, there are two window ports to the outside from the observation deck that I could not match up no matter how much I mess with the location of the hangar deck. (You can see the windows in a scene from "Conscience of the King".) The best I could do is to relocate or add those windows on the outside in a much more forward location....